Junk DNA

Well, I just got banned again at UD, over my response to this post of Barry’s:

In a prior post I took Dr. Liddle (sorry for the misspelled name) to task for this statement:

“Darwinian hypotheses make testable predictions and ID hypotheses (so far) don’t.”

I responded that this was not true and noted that:

For years Darwinists touted “junk DNA” as not just any evidence but powerful, practically irrefutable evidence for the Darwinian hypothesis. ID proponents disagreed and argued that the evidence would ultimately demonstrate function.

Not only did both hypotheses make testable predictions, the Darwinist prediction turned out to be false and the ID prediction turned out to be confirmed

Liddle resonds:

Sorry Barry that that example simply does not work.

Darwinian theory would only predict unused sequences of DNA were it to be the case that unused sequences had no metabolic or other cost . . .

And I will be first in line to cite Darwinian hypotheses that have been falsified. But not the “junk DNA” hypothesis.

Nor will I accept that “no junk DNA” was a positive prediction of ID. It is neither positive, nor is it a prediction.

Dr. Liddle, have you no shame? All I can say is your revisionist history is stunning in its scope and audacity.

Whole books were written by ID proponents about the Darwinist myth of junk DNA. See here.

The ID position has now been largely vindicated and the Darwinist position debunked.

You know that. Therefore, I simply cannot imagine that you assert to the contrary in good faith. If I did not know better, charity would demand that I ascribe your statements to near invincible ignorance. Sadly, that option is not open to me. Therefore, I can only conclude that you are willfully and mendaciously misrepresenting the record.

You made a false statement in the prior post. I posted a second post calling you out. Instead of conceding or retracting you doubled down. Will you double down again or will you retract?

My response was:

Barry, can you cite a scientific paper that makes a prediction, derived from Darwinian theory, that large parts of the genome will be non-functional?

Can you also find an ID paper that predicts that all DNA will be functional?

Can you also find any paper that shows that all DNA is functional?

Would anyone here like to answer my questions?

 

 

80 Replies to “Junk DNA”

  1. Lizzie
    Ignored
    says:

    Mung:
    Elizabeth Liddle:

    The context, of course, is important.

    Elizabeth Liddle:

    Elizabeth Liddle:

    Given that you are “preaching to the choir” here at TSZ, I’m going to bet on the ‘NO’ side of that question.

    Well, I’m rather betting on the NO side myself, but not because TSZ is restricted to people on the “Darwinian” side, because it isn’t.

    Can you answer the questions, Mung?

  2. Alan Fox Alan Fox
    Ignored
    says:

    Commiserations (really congratulations, Lizzie) on forcing Barry to expel you. Though I was surprise how long Barry managed to maintain his “new” open-house moderation policy before reverting to type. As Allan says, “That’ll free up some time for a bit of enabling, then!”

  3. Alan Fox Alan Fox
    Ignored
    says:

    @ mung

    Lizzie’s questions posed to Barry Arrington at UD

    [1]Barry, can you cite a scientific paper that makes a prediction, derived from Darwinian theory, that large parts of the genome will be non-functional?

    [2]Can you also find an ID paper that predicts that all DNA will be functional?

    [3]Can you also find any paper that shows that all DNA is functional?

    1. I don’t know if there is any scientific that predicts large parts of the genome will be non-functional but Larry Moran seems to think not and that the ENCODE consortium as reported was wrong on functionality.

    2. Re an ID paper, obviously not.

    3. If such a paper exists, which I doubt, it would be wrong in its conclusion as there is plenty of evidence for elements in DNA that fulfill no current useful purpose for the organism in the genome such as pseudogenes, transposons, viral elements, etc.

  4. Rumraket Rumraket
    Ignored
    says:

    Mung:
    The question, thorton, which you seem to have missed in your willingness to miss anything not in your ability to comprehend, is as follows:

    Elizabeth Liddle

    HERE, in her question, is HERE at TSZ.

    Then why don’t you get busy answering? You’re HERE after all!

  5. RBH
    Ignored
    says:

    I’ll C&P the comment I left on Sandwalk.

    Larry wrote

    As you know, Barry Arrington claimed that the IDiots made a prediction. They predicted that there’s no such thing as junk DNA. They predicted that most of our genome would turn out to have a function [Let’s Put This One To Rest Please]. That’s much is true. It makes perfect sense because an Intelligent Design Creator wouldn’t create a genome that was 90% junk.

    and then

    This was in response to a claim made by Elizabeth Liddle that Intelligent Design Creationists don’t make predictions. She was wrong about this. I’m not going to defend her on that point.

    We need to distinguish between “intelligent design creationists”–the adherents–and “intelligent design creationism”–the so-called theory. What I suspect Elizabeth meant was that the latter, the so-called theory, doesn’t make predictions. And it doesn’t. I have read Behe, Dembski, Meyer, Luskin, Kenyon, Axe, and more, and I have yet to see a statement of intelligent design “theory” that has anything approaching the level of specificity that would allow one to derive predictions of observations.

    Even you, Larry, slip when you say that “…an Intelligent Design Creator wouldn’t create a genome that was 90% junk.” Sez who? Why not? What constrains agents with the power to design and manufacture biological systems to be economical? Nothing in intelligent design “theory.” Don’t forget that Dembski said that the “aesthetics problem” and the “intentionality problem” are both outside the purview of science: We can’t know what the designer(s) consider beautiful nor whether the designer(s) intended to create economical structures. Maybe the designer(s) like wastage and surplus.

    In order to predict new observations based on some theory that theory has to put clear constraints on what is and is not ‘permitted’–what we should and should not observe under some specified conditions. But Intelligent Design Creationism has no such constraints. Without a detailed characterization of relevant properties of the designing agent(s), IDC has nothing but ad hoc patches pasted on a core of ignorance.

  6. Allan Miller
    Ignored
    says:

    [1]Barry, can you cite a scientific paper that makes a prediction, derived from Darwinian theory, that large parts of the genome will be non-functional?

    Actually, if we are permitted ‘neo-Darwinian”, there is this

    eta: it is wrapped in some commentary from Andas Pellionisz, a dogged critic of junk.

  7. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Allan Miller,

    Thanks, I had never read Ohno’s paper before (though I had heard Ohno speak when he visited our department years after the junk DNA paper).

    It is interesting that, of the three great arguments for the reality of junk DNA, his paper has two of them. It discusses the genetic load, and it mentions the enormous differences in DNA content between species. It does not mention the third — the annotatable families of DNA of dubious value to the organisms, such as transposons, which are seen in the genome. And that omission was simply because we could not sequence DNA in 1969 — sequencing of DNA was not invented for another decade (yes, I know about the sequencing of some RNAs starting in 1968).

    Ohno’s paper holds up pretty well in 2013.

  8. Lizzie
    Ignored
    says:

    Ohno’s prediction that much of the genome will be “junk” is not a prediction of Darwinian evolution.

    It’s a hypothesis that, given the observation rates that mutation rates are very high, yet, phenotypic consequences are small, and that therefore the precise sequence of genome musn’t matter very much.

    It doesn’t predict that the “junk” will have no function – he actually says that it may serve the useful function of spacing out genes.

    And it doesn’t flow from Darwinian theory (it’s not, for instance, the prediction that because mutations are random, there will be lots of random junk around, which wouldn’t make a lot of sense, because if it was costly for organisms to maintain “junk”, then it would be rapidly filtered out).

    So the existence of junk DNA doesn’t “prove” Darwinian evolution, although it is perfectly consistent with it. Nor does it “disprove” ID, because it’s impossible to show that the putative ID had no reason to put it there.

    And the finding (if supported) that at least some of it – even most of it – is functional, would neither falsify Darwinian theory nor support ID.

    It’s actually pretty irrelevant to both, except that within a Darwinian framework it can be used to test further hypotheses, and indeed, it could do the same for ID hypotheses if anyone would actually make one.

    Which is my point. Nobody does.

  9. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Actually, junk DNA does support common ancestry, but it’s not the existence of junk DNA that does that, but the particular patterns found in that junk DNA. Such as the presence of transposon inserts in particular places in two closely-related species. A good example is the sharing of SINE inserts between whales and hippopotamai (yes, that is the correct plural).

    As for the mutation load issue, there is a famous paper by Manfred Eigen and Peter Schuster in Naturwissenschaften in 1971, Among many other interesting things, they argue that with a mutation rate u per base, the genome could not be much more than 1/u bases long. That is under the assumption that all of those sites must be maintained in their states by selection, so it does not count sites where mutations might be neutral. The fact that in most eukaryotes the number of sites is much bigger than 1/u then argues for neutrality at many of those sites.

  10. Allan Miller
    Ignored
    says:

    Lizzie,

    No, of course it does not ‘prove’ Darwinian evolution (whatever that is), but it is a prediction derived from application of the (neo) Darwinian paradigm to the data. A prediction that sequence-dependent function will be the exception rather than the rule, a prediction borne out by the subsequent discovery of transposons and introns.

    Taking the mutational and species-variation arguments together, it predicts that we will find a genome rather poor in essential genes. He does offer a speculation that intergenic spacing may be a function, but there is no need to devote sequence in the proportion 20-to-1 to such a role, nor to vary it so widely across a taxon. So Ohno does predict that we will find predominant non-function IMO, granted that a largely nonfunctional genome is not an expectation of evolutionary theory per se.

  11. Jerad
    Ignored
    says:

    Just to let youse guys and the UD crowd know: I seem to have been banned at UD. This morning my comments were put into moderation and then they disappeared.

    While it is certainly the right of any blog owner to filter the responses they chose to publish (I’ll back down from my censorship charge against KF) one has to wonder what the owners of UD are afraid of.

    Also, aside from their continual inability to come up with a cogent and coherent statement of an ID hypothesis, there is a greater weakness in the ranks: the inablility to address legitimate questions and concerns. My own banning came rapidly on the heals of my my requesting that someone calculate Dr Dembski’s CSI metric for some examples and to hopefully show that it’s not prone to throw up too many false positives or false negatives. While I cannot point to a particular statement that got me banned I’ve got to think that pointing out that for UD to put Dr Dembski’s metric in its glossary but having no one able to compute it was embarrassing at the very least just might have cut too close to the bone. I did also ask Barry many times why he had banned Dr Liddle and that might have been a factor as well.

    I think now that Dr Dawkins and Dr Fox (as stated in a UD post in the last month) are correct: to attempt to engage the most stringent defenders in a dialogue is pointless. I know they will say the same about me but I do think there is a difference in what I acknowledge as data and evidence and what people like Barry and Gil and Mung and KF will grant the same consideration.

    I think one of the reasons the ID crowd are always quick to ascribe to us ‘Darwinists’ a pre-determined ideology is because that’s what they are used to. And they are used to being led and told what is true. To most ID proponents Drs Dembski and Behe are right. Without question. Aside from the fact that to admit they might be wrong would remove one of the few cornerstones of the ID attempt at a hypothesis, there is a deep reluctance to question the figureheads of the movement. Consider how reluctant any ID proponent is to break ranks and speculate on the designer. To not even be able to take a stab at when design was implemented is not only a clear indication of the lack of the explanatory power of ID but it’s also an indication of how tightly the rank and file are held.

    Anyway, have fun trying to keep the dialogue going. I’m going to bow out, for now at least. In the last 5 or 6 years at UD nothing much has changed. The arguments are the same. The attitude is the same (have you looked at their weak arguments against ID? WTF? A school of thought gets to decide what are weak and strong arguments against its precepts???). UD is not about creating a dialogue. If it wasn’t clear before, ever since Denyse came on to do News it’s been pretty clearly a propaganda tool. If you continue to choose to participate in their discussions then make sure you turn your irony meter off first. I wish I could walk away from UD with a more positive impression but I do not feel, at any time, that any of the UD regulars ever seriously considered that I had any significant points to make. I did my best to understand what the ID community was saying but I do not believe that that endeavour was in any way reciprocated.

  12. Lizzie
    Ignored
    says:

    Welcome to TSZ, Jerad! It was good to meet you at UD.

    And I appreciated your moral support.

  13. Alan Fox Alan Fox
    Ignored
    says:

    Jerad,

    Hi Jerad,

    I commend your efforts. Though I did notice a certain, well, cavalier note entering your latest comments. I’ll pass on the news to UD and I think I’ll bow out now, too (yes, this time I mean it – call me on it if I don’t).

    In the last 5 or 6 years at UD nothing much has changed.

    Indeed, except perhaps views have hardened and the tent has shrunk a bit.

    Anyway thanks for letting us know what happened.

    Best wishes
    Alan.

    PS, I know of Richard Dawkins but who’s Dr Fox?

  14. Kantian Naturalist Kantian Naturalist
    Ignored
    says:

    Jerad,

    I’ve decided to stop posting at Uncommon Descent; it’s just not worth my time and energy, especially because I realized that my “writing time” was going to commenting there rather than to working on my book.

    I’ll comment now and again here, insofar as issues raised are relevant to my interests, but by and large I need to be much more careful about how I use my time.

  15. david winter
    Ignored
    says:

    It’s shame the thread was closed without your questions being answered LIzzie.

    The junk DNA “debate” shines a few lights on the so called controversy around ID and evolution.

    Mostly how insular the IDists are. I’m sure the author of the original post at UD thought the conclusion that most of our genomes serve a function was an iron clad finding, and that the best evidence for junk had always been the absence of known function. After all, that’s was Wells said in his book, and the ID sites haveing been repeating ad nauseam ever since. The idea that the best evidnce for our junky genomes still stands, or that the headline results for ENCODE might not make much sense likely never entered his mind.

    The other point, which others have alluded to, is the fact even if “Darwinian” evolutionary biologists didn’t predict junk DNA, evolutionary biology has both developed theories that help us understand it ( especially the (nearly) neutral school) and allow us to test different ideas about junk. Most notably, Lynch’s work on the relationship between genome size and effective population size. As we get more and more genomes to play with, I’m sure we are going to learn a lot more about the dyamics of genome-wide evolution, including the accumulation and loss of junk sequences. I can’t imagine how ID could similarly advance research, even if (a) it had predicted junkless genomes and (b) genomes were junkless!

  16. Lizzie
    Ignored
    says:

    Kantian Naturalist:
    Jerad,

    I’ve decided to stop posting at Uncommon Descent; it’s just not worth my time and energy, especially because I realized that my “writing time” was going to commenting there rather than to working on my book.

    I’ll comment now and again here, insofar as issues raised are relevant to my interests, but by and large I need to be much more careful about how I use my time.

    I sympathise! I use “leechblock” on Firefox now, which helps! But trying to keep up with complicated discussions on several boards simultaneously is certainly a time leech!

    I’ve really enjoyed your posts, and have learned a lot. I hope you will look in from time to time in the future as well.

    Lizzie

  17. Kantian Naturalist Kantian Naturalist
    Ignored
    says:

    Lizzie,

    Oh my stars and garters! Oh my ears and whiskers! Leechblock is the app I’ve been needing since 1998! Oh what a glorious day! Thank you so much!

  18. Flint
    Ignored
    says:

    Lizzie,

    Seems clear that your offense was in the posture you adopted toward a key part of the ID catechism. In their world, yes, Darwinian theory predicts lots of it and ID theory predicts the opposite. This is to be accepted as a matter of doctrine, not questioned simply because there is no evidential support for either “prediction”.

    Just consider Barry’s response, where he simply claims as a matter not to be questioned that his doctrine is Truth. It’s telling that he asserts that nobody can disagree with him in good faith. Mere facts and evidence don’t count.

    But the rather meaningless claim that “ID predicts no junk DNA” is something even Barry recognizes is as close to a fig leaf as ID can get, scientifically speaking. It’s not something up for discussion, it’s just the best available excuse to ban a nonbeliever.

  19. petrushka
    Ignored
    says:

    Why does ID predict No Junk?

    Isn’t that a bit like predicting no death, no extinction, no vestigial bits?

  20. Mark Frank
    Ignored
    says:

    Is there an equivalent to Leechblock for Chrome? Even better – a program that selectively filters UD comments according to the author.

  21. equate65
    Ignored
    says:

    Jerad, according to BA you were not banned, just put in Mod. Also, for the record bornagain77 and Joe G have also been banned at different times in the past, then reinstated at a later date, as EL has been in the past. Also, there are many ID proponents, including myself, who don’t agree with EL’s ban, and are on record at UD stating so..

  22. Lizzie
    Ignored
    says:

    Thank you, equate65.

  23. petrushka
    Ignored
    says:

    Moderation at UD is effectively a ban. First, it prevents you from participating in a thread, because it can be days befor your comments appear, and everyone has passed pay that part of the argument.

    Second, it punishes you for expressing opinions. Just pathetic.

    Joseph was banned and re-registered as JoeG. Not the first time he has done this. If anyone else tried to get around a ban by transparently registering under a new name, they would be banned again for violating the rules.

    Joe was banned not for expressing opinions, but for vulgar language and vulgarity in general. Not a particularly dishonest reason. Different sites have different tolerances for vulgarity. I find it amusing that UD tolerates nearly unlimited vulgarity from Joe, but not from anyone else.

    ETA. I suppose this post needs to be moved to the sandbox.

  24. Lizzie
    Ignored
    says:

    I have to say, I find “is no longer with us” cringe-making.

    What’s wrong with saying “I banned X because of Y”?

    Long live E-prime.

  25. Patrick Patrick
    Ignored
    says:

    Lizzie:
    I have to say, I find “is no longer with us” cringe-making.

    What’s wrong with saying “I banned X because of Y”?

    Long live E-prime.

    What’s wrong is that saying “I banned Lizzie because her education, intelligence, tenaciousness, politesse, and poise demonstrated the utter lack of any scientific merit for our views and made us embarrassed to look our mothers in the eyes.” would destroy Barry’s already fragile self-esteem.

  26. Claudiu Bandea
    Ignored
    says:

    I just left the following comment on ‘junk DNA’ at a different site and I thought it might also be of interest to readers here at The Skeptical Zone:

    The idea that most of the genome in species with high c-value has informational roles has been first questioned many decades ago, and since then basically abandoned by most researchers studying the evolution of genome size. Therefore, it would make little sense to keep refuting this idea in endless posts and discussions; it’s like beating a dead horse.

    I think, it would make more sense to evaluate and discuss the ideas and opinions as expressed by the current experts on genome size evolution and the so called ‘junk DNA’ (jDNA), including Thomas Cavalier-Smith, Ford Doolittle and Ryan Gregory who support non-informational functions for jDNA.

    Here is an excerpt from a paper on jDNA published this year by Ford Doolittle (Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE”; Proc Natl Acad Sci U S A. 110:5294-300):

    “Cavalier-Smith (13, 20) called DNA’s structural and cell biological roles “nucleoskeletal,” considering C-value to be optimized by organism-level natural selection (13, 20). Gregory, now the principal C-value theorist, embraces a more “pluralistic, hierarchical approach” to what he calls “nucleotypic” function (11, 12, 17)”.

    And here are excerpts from Ryan Gregory’s papers:

    “Although some researchers continue to characterize much variation in genome size as a mere by-product of an intragenomic selfish DNA “free-for-all” there is increasing evidence for the primacy of selection in molding genome sizes via impacts on cell size and division rates” (Gregory TR, Hebert PD. 1999. The modulation of DNA content: proximate causes and ultimate consequences. Genome Res; 9(4):317-24).

    “These are the “nucleoskeletal” and “nucleotypic” theories which, though differing substantially in their specifics, both describe genome size variation as the outcome of selection via the intermediate of cell size” (Gregory TR. 2004. Insertion-deletion biases and the evolution of genome size. Gene, 324:15-34).

    Clearly, these scientists describe genome size variation as the outcome of selection via the intermediate of cell size, and as emphasized by Doolittle in the conclusion of his paper: by developing a “larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon … much that we now call junk could then become functional.” (see reference above).

    Therefore, the current thinking by the scholars in the field of genome size evolution and c-value enigma, support the perspective that most of the genome in species with high c-value is functional.

  27. Allan Miller
    Ignored
    says:

    Claudiu Bandea,

    Therefore, the current thinking by the scholars in the field of genome size evolution and c-value enigma, support the perspective that most of the genome in species with high c-value is functional.

    Gregory is not a strong advocate of this view IMO. From his blog: “By contrast, we do not have strong evidence that non-coding DNA is functional or what it may be functional for.”. Perhaps this turns on what one means by ‘functional’ – ‘has an effect’ or ‘is there due to adaptation’.

  28. Claudiu Bandea
    Ignored
    says:

    Allan,

    I agree, in his blog Gregory dismisses the idea jDNA has informational functions; however, he has spent much of his scientific career developing the nucleotypic hypothesis on the evolution of genome size as described in the excerpts from his publications (see above), which BTW are of very high scholarly value and should be mandatory reading for all students of genome evolution.

  29. Claudiu Bandea
    Ignored
    says:

    You can read Ryan Gregory’s response to my comment above at: http://sandwalk.blogspot.com/2013/10/non-darwinian-evolution-in-1969-case.html#comment-form

  30. Mung Mung
    Ignored
    says:

    Not only is “junk DNA” an inappropriate moniker for noncoding DNA in general because of the minority status of pseudogenes within genome sequences, but it also has the unfortunate consequence of instilling a strong a priori assumption of total nonfunction.

    The Evolution of the Genome

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